JTE can be used to apply a pipeline template to an entire repository by creating a Multibranch Project.
To configure this, under the Build Configuration you will set the mode as
Jenkins Templating Engine
Jenkins Templating Engine is selected, a checkbox option is presented to exclude branches in source code repositories that do not have a
pipeline_config.groovy file at the root of the repository.
The default value is to create pipeline jobs for every branch regardless of whether a
pipeline_config.groovy is present or not.
Note, the Multibranch Project type can configure a Governance Tier for specifying pipeline templates, library sources, and applying a pipeline configuration to the entire repository.
You can find these settings under the
Jenkins Templating Engine section of the job configuration.